First, and most important, you can now see up to 90 days of historical data. If you click on the date picker in the top right of Search queries, you can go back three months instead of the previous 35 days.
And after you click:
In order to see 90 days, the option to view with changes will be disabled. If you want to see the changes with respect to the previous time period, the limit remains 30 days. Changes are disabled by default but you can switch them on and off with the button between the graph and the table. Top search queries data is normally available within 2 or 3 days.
Another big improvement in Webmaster Tools is that you can now see basic search query data as soon as you verify ownership of a site. No more waiting to see your information.

Finally, we're now collecting data for the top 2000 queries for which your site gets clicks. You may see less than 2000 if we didn’t record any clicks for a particular query in a given day, or if your query data is spread out among many countries or languages. For example, a search for [flowers] on Google Canada is counted separately from a search for [flowers] on google.com. Nevertheless, with this change 98% of sites will have complete coverage. Let us know what you think. We hope the new data will be useful.